Atomic force microscopy (AFM) has proven itself to be a powerful and diverse tool for the study of microbial systems on both single and multicellular scales including complex biofilms. This chapter will review how AFM and its derivatives have been used to unravel the nanoscale forces governing the structure and behavior of biofilms, thus providing unique insight into the control of microbial populations within clinical and industrial environments. Diversification of AFM-based technologies has allowed for the creation of a truly multiparametric platform, enabling the interrogation of all aspects of microbial systems. Advances in traditional AFM operation have allowed, for the first time, insight into the topographical landscape of both microbial cells and spores, which, when combined with high-speed AFM's ability to resolve the structure of surface macromolecules, have provided, with unparalleled detail, visualization of this complex environmental interface. The application of AFM force spectroscopies has enabled the analysis of many microbial nanomechanical properties including macromolecule folding pathways, receptor ligand binding events, microbial adhesion forces, biofilm mechanical properties, and antimicrobial/antibiofilm affectivities. Thus, AFM has offered an outstanding glimpse into the biofilm, how its inhabitants create and use this complex adaptive interface, and perhaps most importantly what can be done to control this.